Ideally, there should be a record created for the father. Everyone has/had one, even if the details are unknown. Having a record for them allows you (or someone else) to add sketchy details if and when they surface. This could be anything from full biographical details, to a simple birth date, to a vague mention in some document. Many years down the line, another researcher may be able to make a good case for the father's identify based on the accumulated sketchy details.
There are a couple of caveats, though. The GEDCOM representation of family trees allows either parent, or both, to be absent in the data. This can cause problems in some software. Also, if the name of a person is unknown then you should resist inserting a pseudo-name, such as "Unknown", "None", "LNU" (last name unknown), etc. Products should have a special way of indicating an unknown name (incl. leaving it blank) but some others will force you to provide something in the name field. Tamura Jones has a very good article on the woes of adding pseudo-names into a real-name field.